estimateParameter           package:CALIB           R Documentation

_E_s_t_i_m_a_t_e _m_o_d_e_l _p_a_r_a_m_e_t_e_r _f_r_o_m _s_p_i_k_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Estimate the calibration model parameters according to the known
     concentration and  the measured intensities of external control
     spikes on each array.

_U_s_a_g_e:

      estimateParameter(spike, RG, bc = FALSE, area = TRUE, errormodel = "M")

_A_r_g_u_m_e_n_t_s:

   spike: a 'SpikeList' object.

      RG: a 'RGList_CALIB' object.

      bc: a logical value. 'TRUE' means background corrected measured 
          intensities are used. Default is 'FALSE'.

    area: a logical value. 'TRUE' means spot area is used to calculate 
          measured intensities. Namly, measured intensities are
          calculated by  foreground intensities(or background corrected
          intensities, if bc is  'TRUE' ) multiply spot area. 'FALSE'
          means spot area is not used. Default is 'TRUE' .

errormodel: a character to indicate the distribution of spot capacity. 
          "A" means spot capacity is additive. "M" means spot capacity
          is multiplicative. Default is "M". 

_D_e_t_a_i_l_s:

     This function estimates calibration model parameters. In this
     function,  the model parameters are estimated separately for each
     microarray,  based on the measured intensities of the external
     control spikes and  their known concentration in the hybridization
     solution. It accepts  spike measured intensities and concentration
     from 'spike' argument,  which is an object of 'SpikeList' class. 

     It supports different ways to calculate the measured intensities. 
     Arguments 'bc' and 'area' are logical and their combinations is
     used  for specifying four differents ways. 'bc' indicates using
     background correction or not. 'area' indicates multiplying spot
     area or not. The default value of these two arguments are 'bc' =
     FALSE and 'area' = TRUE. 

     The argument 'errormodel' is to specify the distribution of spot
     capacity  of each array. The spot capacity is either additive or
     multiplicative. Whichever distribution is more appropriate will
     depend largely on the type of  microarray slide and spotting
     procedure used. The spot parameters mus and sigmas can be
     considered equal for all measurements of a single array.

     The argument 'RG' is for calculating the maximum intensity of each
     array. These  maximum intensities are used to estimate the upper
     saturation level of each array.

     More details please refer to the reference literature.

_V_a_l_u_e:

     An 'ParameterList' object containing the components:

     MuS: matrix containing MuS for each array.

      Ka: matrix containing Ka for each array.

      P1: matrix containing P1 of each dye for each array.  

      P2: matrix containing P2 of each dye for each array.

  SigmaA: matrix containing sigma additive for each array.

  SigmaM: matrix containing sigma multiplicative for each array.

  SigmaS: matrix containing sigma spoterror for each array.

SpotError: matrix containing the spot error of each spot for each
          array. 

  Method: boolean values indicating the way to calculate the measured
          intensities.

ErrorModel: character '"M"' or '"A"' to indicate the type of spot 
          capacity distribution.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006)  A
     calibration method for estimating absolute expression levels from 
     microarray data. Bioinformatics  22: 1251-1258.

_E_x_a_m_p_l_e_s:

     # load data: RG and spike
     data(RG)
     data(spike)

     # for the measured itensities, take the default bc=FALSE and area=TRUE.
     # use multiplicative spot error model
     parameter <- estimateParameter(spike,RG)

